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The University of Chicago Epistasis, Contingency, And THE UNIVERSITY OF CHICAGO EPISTASIS, CONTINGENCY, AND EVOLVABILITY IN THE SEQUENCE SPACE OF ANCIENT PROTEINS A DISSERTATION SUBMITTED TO THE FACULTY OF THE DIVISION OF THE BIOLOGICAL SCIENCES AND THE PRITZKER SCHOOL OF MEDICINE IN CANDIDACY FOR THE DEGREE OF DOCTOR OF PHILOSOPHY GRADUATE PROGRAM IN BIOCHEMISTRY AND MOLECULAR BIOPHYSICS BY TYLER NELSON STARR CHICAGO, ILLINOIS AUGUST 2018 Table of Contents List of Figures .................................................................................................................... iv List of Tables ..................................................................................................................... vi Acknowledgements ........................................................................................................... vii Abstract .............................................................................................................................. ix Chapter 1 Introduction ......................................................................................................1 1.1 Sequence space and protein evolution .............................................................1 1.2 Deep mutational scanning ................................................................................2 1.3 Epistasis ...........................................................................................................3 1.4 Chance and determinism ..................................................................................4 1.5 Evolvability ......................................................................................................6 1.6 Ancestral protein reconstruction ......................................................................6 1.7 Research questions and approach ....................................................................7 Chapter 2 Epistasis in protein evolution .........................................................................10 2.1 Summary ........................................................................................................10 2.2 Introduction ....................................................................................................11 2.3 Epistasis and protein sequence space .............................................................13 2.4 Prevalence and strength of epistasis ..............................................................15 2.4.1 Epistasis in a protein’s local sequence neighborhood ......................15 2.4.2 Epistasis in long-term protein evolution ..........................................17 2.5 Specificity of epistasis and causal mechanisms .............................................24 2.5.1 Specific epistasis ..............................................................................25 2.5.2 Nonspecific epistasis ........................................................................28 2.5.3 Specific positive versus nonspecific negative epistasis ...................31 2.5.4 Specific and nonspecific epistasis in long-term evolution ...............32 2.6 Evolutionary implications of epistasis ...........................................................34 2.6.1 Evolvability and robustness ..............................................................34 2.6.2 Historical contingency ......................................................................35 2.6.3 Reversibility .....................................................................................36 2.6.4 Long-term evolutionary constraints .................................................37 2.7 Conclusions and future directions ..................................................................38 Chapter 3 Pervasive contingency and entrenchment in a billion years of Hsp90 evolution ........................................................................................................42 3.1 Summary ........................................................................................................42 3.2 Introduction ....................................................................................................43 3.3 Results ............................................................................................................45 3.3.1 The historical trajectory of Hsp90 sequence evolution ....................45 3.3.2 Entrenchment and irreversibility ......................................................46 ii 3.3.3 Intramolecular versus intermolecular epistasis ................................47 3.3.4 Contingency and permissive substitutions .......................................50 3.3.5 Specificity of epistatic interactions ..................................................51 3.4 Discussion ......................................................................................................56 3.4.1 Relation to prior work ......................................................................56 3.4.2 Limitations ........................................................................................57 3.4.3 Implications ......................................................................................58 3.5 Methods..........................................................................................................59 Chapter 4 Alternative evolutionary histories in the sequence space of an ancient protein ............................................................................................................72 4.1 Summary ........................................................................................................72 4.2 Introduction ....................................................................................................73 4.3 Results ............................................................................................................75 4.3.1 Deep mutational scanning of an ancient evolutionary transition .....75 4.3.2 The historical outcome is not unique in its function ........................76 4.3.3 The historical outcome is not unique in its accessibility ..................77 4.3.4 The historical starting point is not unique in its evolvability ...........80 4.3.5 Historical permissive substitutions are broadly permissive .............81 4.4 Discussion ......................................................................................................85 4.5 Methods..........................................................................................................88 Chapter 5 Epistasis and evolvability in a protein sequence-function landscape ..........105 5.1 Summary ......................................................................................................105 5.2 Introduction ..................................................................................................105 5.3 Results & Discussion ...................................................................................108 5.3.1 A global model of the sequence-function landscape ......................108 5.3.2 The genetic determinants of ERE- and SRE-binding .....................113 5.3.3 Partitioning the determinants of ERE- and SRE-binding ...............118 5.3.4 Epistatic and main-effect terms synergize to cause single-step transitions in specificity ..................................................................122 5.4 Conclusions and Future Directions ..............................................................125 5.5 Methods........................................................................................................127 Chapter 6 Conclusion ...................................................................................................130 Appendix 1 Supplementary figures for Chapter 3 ..........................................................133 Appendix 2 Supplementary figures and tables for Chapter 4 .........................................144 Bibliography ...................................................................................................................156 iii List of Figures Figure 2.1. Patterns of epistasis between mutations ......................................................................11 Figure 2.2. Evidence for epistasis in extant sequence data ............................................................20 Figure 2.3. Mechanisms of epistasis and their evolutionary implications .....................................25 Figure 2.4. Examples of specific and nonspecific epistasis ...........................................................26 Figure 3.1. Ancestral states are deleterious in the yeast Hsp90 NTD ............................................45 Figure 3.2. Fitness effects of substitutions are modified by intramolecular epistasis ...................48 Figure 3.3. Widespread contingency and entrenchment ................................................................51 Figure 3.4. Epistatic interactions are specific ................................................................................52 Figure 3.5. A daisy-chain model of epistasis .................................................................................55 Figure 4.1. Diverse sequences and mechanisms can yield the derived DNA specificity ..............74 Figure 4.2. Evolvability of SRE specificity in an ancestral sequence space .................................79 Figure 4.3. Historical permissive substitutions broadly enhanced evolvability ............................83 Figure 4.4. The effect of historical permissive substitutions is mediated by nonspecific increases in affinity ............................................................................................................................85
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